Initial steps may include performing a PSI-BLAST or PatternHunter search to locate a similar sequences with a known structure in the Protein Data Bank (PDB).
If there is no homology found, the researcher must perform either X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy, both of which require considerable time and resources to yield a structure.
The integer programming approach to RAPTOR produces higher quality models than other protein threading methods.
Most threading software use dynamic programming to optimize their scoring functions when aligning a sequence with a template.
Pairwise contacts are very conserved in protein structure and crucial for prediction accuracy.
NoCore, NPCore and IP are the three different threading engines implemented in RAPTOR.
To make it a comprehensive tool set, PSI-BLAST is also included in RAPTOR to let people do homology modeling.
For each template, people can view the alignment, E-value and numerous other specific scores.
CASP, Critical Assessment of Techniques for Protein Structure Prediction, is a biennial experiment sponsored by NIH.
CASP represents the Olympic Games of the protein structure prediction community and was established in 1994.
RAPTOR first appeared in CAFASP3 (CASP5) in 2002 and was ranked number one in the individual server group for that year.
Since then, RAPTOR has actively participated in every CASP for evaluation purpose and been consistently ranked in the top tier.